MargheRita: an R package for LC-MS/MS SWATH metabolomics data analysis and confident metabolite identification based on a spectral library of reference standards

Untargeted metabolomics allows acquisition of thousands metabolite signals in a single sample that demands computational techniques for post-acquisition steps. Web-based data processing solutions as well as R packages exist and provide tools for metabolomics data analysis. Frequently these tools cover only a part of the entire workflow thus requiring the use of different platforms. Moreover, despite the existence of several databases, metabolite identification remains the bottleneck in metabolomics due to the high variability in the fragmentation pattern resulting from different mass spectrometer configuration-based libraries.

margheRita covers the whole data analysis workflow in LC-MS/MS untargeted metabolomics experiments, using MS and MS/MS (even SWATH) data. It takes in input the results of data extraction generated by MS-Dial [@Tsugawa2015] and metadata for sample processing (in text or Excel format).

The package provides:

a series of pre-processing functions (quality control, filtering and normalization) with a particular focus on methods specifically recommended for metabolomic profiles, such as filtering by mass defects, filtering by coefficient of variation (samples vs QCs) and probabilistic quotient normalization;
metabolite annotation up to level-1, based on in-house spectral libraries as well as freely available libraries;
spectral libraries that covers 4 different chromatographic column types: RP-C18, HILIC, RP-C8 and pZIC-HILIC Zwitterionic.
simplified execution of parametric and non-parametric statistical tests over a large number of features;
pathway analysis based on ORA and MSEA over various databases.

Documentation: https://emosca-cnr.github.io/margheRita

Source code: https://github.com/emosca-cnr/margheRita

Citation: Ettore Mosca, Marynka Ulaszewska, Zahrasadat Alavikakhki, Edoardo Niccolò Bellini, Valeria Mannella, Gianfranco Frigerio, Denise Drago, Annapaola Andolfo. MargheRita: an R package for LC-MS/MS SWATH metabolomics data analysis and confident metabolite identification based on a spectral library of reference standards. bioRxiv 2024.06.20.599545; doi: https://doi.org/10.1101/2024.06.20.599545

Contacts:

Annapaola Andolfo, Proteomics and Metabolomcis Facility, HSR
Ettore Mosca, Bioinformatics Lab, CNR-ITB

Installation

See https://emosca-cnr.github.io/margheRita/articles/margheRita.html